Research workbench
Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and fanci
Analyse Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and fanci in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AY1
- Type
- protein + DNA
- Length
- 3,138 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fanconi anemia group I protein; Fanconi anemia group D2 protein; Ubiquitin-60S ribosomal…
- EC
- 3.4.19.12
- UniProt
- Q9NVI1, Q9BXW9, P62987, O94782, Q8TAF3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 6 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fanconi anemia group I protein | protein | 1033 | 68% helix, 2% strand | Q9NVI1 |
| B | Fanconi anemia group D2 protein | protein | 1033 | 68% helix, 1% strand | Q9BXW9 |
| C | Ubiquitin-60S ribosomal protein L40 | protein | 77 | 21% helix, 32% strand | P62987 |
| D | Ubiquitin carboxyl-terminal hydrolase 1 (EC 3.4.19.12) | protein | 341 | 33% helix, 24% strand | O94782 |
| E | Wd repeat-containing protein 48 | protein | 596 | 12% helix, 40% strand | Q8TAF3 |
| S, T | DNA (61-mer) | dna | 29 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.81 | 0.83 | 79 | empty |
| 2 | 876 | 0.73 | 0.78 | 67 | empty |
| 3 | 330 | 0.70 | 0.83 | 40 | empty |
| 4 | 618 | 0.69 | 0.78 | 62 | empty |
| 5 | 670 | 0.69 | 0.77 | 64 | empty |
Interfaces
11 interfaces between chains.
- A–B · 3429 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1957 Ų buried · 31 hydrogen bonds · protein-protein
- A–E · 1656 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 812 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 660 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 isopeptide (disulfide, isopeptide).
Compared structures
- 7AY1 · Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI · the same entry in another collection · chain T against T, TM-score 1.00
- Q8TAF3 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 48 (Q8TAF3) · a predicted model of the same protein · chain E against A, TM-score 0.98
- O94782 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 1 (O94782) · a predicted model of the same protein · chain D against A, TM-score 0.96
- Q9NVI1 · AlphaFold monomer V2.0 prediction for fanconi anemia group I protein (Q9NVI1) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P62987 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P62987) · a predicted model of the same protein · chain C against A, TM-score 0.90
- Q9BXW9 · AlphaFold monomer V2.0 prediction for fanconi anemia group D2 protein (Q9BXW9) · a predicted model of the same protein · chain B against A, TM-score 0.82
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NVI1
- Every structure of UniProt Q9BXW9
- Every structure of UniProt P62987
- Every structure of UniProt O94782
- Every structure of UniProt Q8TAF3
- Elsewhere: RCSB PDB 7AY1 · PDBe 7AY1 · UniProt Q9NVI1 · UniProt Q9BXW9 · UniProt P62987 · UniProt O94782 · UniProt Q8TAF3
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